From 191efc014006299733588b8b9ab7108184ef0445 Mon Sep 17 00:00:00 2001
From: OganM <ogan.mancarcii@gmail.com>
Date: Thu, 12 Sep 2024 17:34:09 -0700
Subject: [PATCH] bring back gene symbol support

---
 DESCRIPTION  |  2 +-
 R/ermineR.R  | 18 ++++++++++++++++--
 R/miscFuns.R |  8 +++++++-
 3 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f893d48..2a4c82f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ermineR
 Title: Gene set analysis with multifunctionality assessment
-Version: 1.0.1.9000
+Version: 1.0.2.9000
 Authors@R: person("Ogan", "Mancarci", email = "ogan.mancarci@gmail.com", role = c("aut", "cre"))
 Description: ErmineR is an interface to the ermineJ gene set analysis software (http://erminej.msl.ubc.ca). 
 Depends: R (>= 3.4.0)
diff --git a/R/ermineR.R b/R/ermineR.R
index 68d3819..967527a 100644
--- a/R/ermineR.R
+++ b/R/ermineR.R
@@ -69,7 +69,7 @@ ermineR = function(annotation = NULL,
     } else{
         nullAnnot = FALSE
     }
-    if('character' %in% class(annotation)){
+    if('character' %in% class(annotation) && !grepl('Generic_[a-z]*$',annotation)){
         if(!file.exists(annotation)){
             message('Attempting to download annotation file')
             annoTemp = tempfile()
@@ -85,7 +85,21 @@ ermineR = function(annotation = NULL,
             annotation = annoTemp
             
         }
-    } else if('data.frame' %in% class(annotation)) {
+    }else if('character' %in% class(annotation) && grepl('Generic_[a-z]*$',annotation)){
+        
+        annot = tryCatch(suppressWarnings(gemma.R::get_platform_annotations(platform = paste0(annotation,'_ncbiIds'),
+                                                                    annotType = 'noParents',
+                                                                    memoised = FALSE,
+                                                                    unzip = TRUE)),
+                 error = function(e){
+                     stop('"annotation" is not a valid file or exists in Pavlidis lab annotations. Use listGemmaAnnotations() to get a list of available annotations.')
+                 })
+        annot$ElementName = annot$GeneSymbols
+        temp = tempfile()
+        annot %>% readr::write_tsv(temp)
+        annotation = temp
+        
+    }else if('data.frame' %in% class(annotation)) {
         temp = tempfile()
         annotation %>% readr::write_tsv(temp)
         annotation = temp # replace the annotation object with the newly created file name
diff --git a/R/miscFuns.R b/R/miscFuns.R
index 987e87d..b9f7ac3 100644
--- a/R/miscFuns.R
+++ b/R/miscFuns.R
@@ -8,7 +8,13 @@ listGemmaAnnotations = function(){
     annots = httr::GET('https://gemma.msl.ubc.ca/annots/')$content %>% rawToChar() %>% XML::getHTMLLinks() %>% 
         {.[grepl('noParents',.)]} %>% stringr::str_extract('.*?(?=_noParents)')
     
-    return(annots)
+    platforms = gemma.R::get_platforms_by_ids() %>% gemma.R::get_all_pages()
+    generics = platforms$platform.shortName %>%
+        grepl('Generic_[a-z]*_ncbiIds',.) %>% 
+        {platforms$platform.shortName[.]}
+    
+    
+    return(c(platforms$platform.shortName,generics %>% gsub('_ncbiIds','',.)))
 }